Residents shared photographs on social media of water pooling inside their homes.
Disaster Risk Management spokesperson Charlotte Powell said on Wednesday: "Due to last night's heavy downpours, localised flooding has occurred in informal settlements and formal areas across the metropole.
"Informal settlements affected are in K, SST and BM Section, Makhaza, Khayelitsha, Langa, Philippi, Gugulethu and Imizamo Yethu in Hout Bay.
There were, however, no evacuations.
Formal areas affected by flooding included Athlone, Gatesville, Diep River and Wallacedene.
In Manenberg, a canal overflowed, leading to a number of houses being flooded.
"Various city departments are making assessments and will continue the mop-up operations that have been ongoing since the cold front hit," said Powell.